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Tobacco mild green mosaic virus (TMGMV)-like nanocarriers were designed for gene delivery to plant cells. High aspect ratio TMGMVs were coated with a polycationic biopolymer, poly(allylamine) hydrochloride (PAH), to generate highly charged nanomaterials (TMGMV-PAH; 56.20 ± 4.7 mV) that efficiently load (1:6 TMGMV:DNA mass ratio) and deliver single-stranded and plasmid DNA to plant cells. The TMGMV-PAH were taken up through energy-independent mechanisms in Arabidopsis protoplasts. TMGMV-PAH delivered a plasmid DNA encoding a green fluorescent protein (GFP) to the protoplast nucleus (70% viability), as evidenced by GFP expression using confocal microscopy and Western blot analysis. TMGMV-PAH were inactivated (iTMGMV-PAH) using UV cross-linking to prevent systemic infection in intact plants. Inactivated iTMGMV-PAH-mediated pDNA delivery and gene expression of GFP in vivo was determined using confocal microscopy and RT-qPCR. Virus-like nanocarrier-mediated gene delivery can act as a facile and biocompatible tool for advancing genetic engineering in plants.

ABSTRACT Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open‐source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating and organising sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity. The primer module designs universal primers for downstream applications. Finally, a visualisation pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we identified 30 plastid intergenic spacers. These spacers exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, highlighting the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilisation of organelle genomic data and broaden the prospects for related research endeavours. [ABSTRACT FROM AUTHOR]

Microbiomes play a crucial role in plant health, aiding nutrient acquisition and enhancing stress tolerance in C3 and C4 plants. While past microbiome research focused on the C3 model plant Arabidopsis (Arabidopsis thaliana), recent attention has shifted towards C4 food and biofuel crops such as maize, millet, sorghum, switchgrass, and miscanthus. Similar to C3 plant microbiome assembly, C4 plant microbiome assembly is influenced by environmental factors, such as drought and nutrient availability, as well as plant genetics. Root and shoot microbiomes of C4 cereal plants can extend diverse plant phenotypes of agronomic importance, including tolerance to drought and nitrogen stress, and enhanced yield. Foxtail millet, a climate-resilient crop, holds promise as a model for C4 plant microbiome research due to its small, well-annotated genome and versatile genetic resources. Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research. [ABSTRACT FROM AUTHOR]

The investigation was carried out during rabi season (November-April) of 2020-2021 in the polyhouse, Department of Genetics and Plant Breeding, Lovely Professional University, Phagwara, Punjab, India to assess the performance of chickpea genotypes under salinity stress conditions. The experiment was conducted using a Completely Randomized Design (CRD) with three replications under two conditions: saline (pots without holes) and control (pots with holes). Twenty genotypes were collected out of which seventeen from ICRISAT, Hyderabad and three from ARS, SriGanganagar. The salinity stress was created using salts NaCl, which were administered in split doses of 60 mM at the time of sowing and 15 DAS. The study monitored various parameters such as phenological, physiological, morphological, biochemical, and yield parameters to determine the effect of salt stress on genotypes exhibiting different tolerance levels. The results showed that the total proline content increased due to the production of stress-related proteins during salinity stress. However, the yield parameters were reduced under stress conditions, with the highest decrease observed in the 60 mM NaCl treatment group compared to the control group. Based on the results of the study, ICC5439 and GNG 1581 are highly tolerant chickpea genotypes under salinity stress conditions. ICC 6050, ICC 251, ICC 252, and ICC 262 are medium tolerant genotypes, while ICC253, ICC 247, and ICC 249 are highly susceptible genotypes. Remaining are minimum tolerant and sensitive genotypes. [ABSTRACT FROM AUTHOR]

Despite our emergent understanding of the contribution of beneficial microbes to the health of humans and the crops we eat, microbiome engineering to improve plant health has had limited success. Recent work has shown that plant genotype plays a critical role in shaping the plant microbiome and so plant genetics must be considered in engineering practices. Here, we review recent work from our lab and others on plant-driven genetic and molecular mechanisms that shape plant-associated microbial communities. Based on our emergent understanding of plant-driven recruitment of beneficial microbes, we discuss challenges in Canadian agriculture that are strong candidates for microbiome engineering. These include pathogens that have been difficult to control through traditional methods including root rot pathogens, as well as controlled agricultural systems like greenhouses and vertical farming. Finally, we discuss knowledge gaps to achieve successful microbiome engineering that can be filled with basic research, particularly through the use of model plant systems. [ABSTRACT FROM AUTHOR]

Over the last 10 years, global raspberry production has increased by 47.89%, based mainly on the red raspberry species (Rubus idaeus). However, the black raspberry (Rubus occidentalis), although less consumed, is resistant to one of the most important diseases for the crop, the late leaf rust caused by Acculeastrum americanum fungus. In this context, genetic resistance is the most sustainable way to control the disease, mainly because there are no registered fungicides for late leaf rust in Brazil. Therefore, the aim was to understand the genetic architecture that controls resistance to late leaf rust in raspberries. For that, we used an interspecific multiparental population using the species mentioned above as parents, 2 different statistical approaches to associate the phenotypes with markers [GWAS (genome-wide association studies) and copula graphical models], and 2 phenotyping methodologies from the first to the 17th day after inoculation (high-throughput phenotyping with a multispectral camera and traditional phenotyping by disease severity scores). Our findings indicate that a locus of higher effect, at position 13.3 Mb on chromosome 5, possibly controls late leaf rust resistance, as both GWAS and the network suggested the same marker. Of the 12 genes flanking its region, 4 were possible receptors, 3 were likely defense executors, 1 gene was likely part of signaling cascades, and 4 were classified as nondefense related. Although the network and GWAS indicated the same higher effect genomic region, the network identified other different candidate regions, potentially complementing the genetic control comprehension. [ABSTRACT FROM AUTHOR]

Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding. Previously, we have established H. incana as the model plant for high photosynthetic light-use efficiency (LUE). Now we aim to unravel the genetic basis of this trait in H. incana , potentially contributing to the improvement of photosynthetic LUE in other species. Here, we compare its transcriptomic response to high light with that of Arabidopsis thaliana , Brassica rapa , and Brassica nigra , 3 fellow Brassicaceae members with lower photosynthetic LUE. We built a high-light, high-uniformity growing environment, in which the plants developed normally without signs of stress. We compared gene expression in contrasting light conditions across species, utilizing a panproteome to identify orthologous proteins. In-depth analysis of 3 key photosynthetic pathways showed a general trend of lower gene expression under high-light conditions for all 4 species. However, several photosynthesis-related genes in H. incana break this trend. We observed cases of constitutive higher expression (like antenna protein LHCB8), treatment-dependent differential expression (as for PSBE), and cumulative higher expression through simultaneous expression of multiple gene copies (like LHCA6). Thus, H. incana shows differential regulation of essential photosynthesis genes, with the light-harvesting complex as the first point of deviation. The effect of these expression differences on protein abundance and turnover, and ultimately the high photosynthetic LUE phenotype is relevant for further investigation. Furthermore, this transcriptomic resource of plants fully grown under, rather than briefly exposed to, a very high irradiance, will support the development of highly efficient photosynthesis in crops. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic presented significant challenges for both students and educators, particularly because of the virtualization of classes and the consequent lack of practical sessions following the closure of laboratories and experimental fields in universities. The absence of interaction among students and practical classes led to a diminished interest in studies, as students found it difficult to connect theoretical knowledge with practical application. This study explores the implementation of a Journal Club (JC) as a collaborative-metacognitive use of the science literature teaching approach (CMSLTA) to enhance theoretical and practical knowledge through the reading and discussion of scientific literature in an e-learning environment. In this approach, students read scientific articles, write essays, and engage in group discussions. The methodology was applied over two consecutive academic semesters in 2021 and 2022 within plant genetics courses. Academic achievement was evaluated through essay assessments, and surveys were conducted at the end of each semester. The results revealed notable progress in student grades throughout the semester, with over 80% of participants endorsing JC implementation and recognizing its relevance to their education. The Journal Club facilitated the integration of theoretical knowledge covered in lectures and equipped students with various digital research tools. [ABSTRACT FROM AUTHOR]

This article presents a study that compares different techniques for estimating gene copy numbers in genetically modified crops. The researchers evaluated Southern blotting, qPCR, dPCR, and PE-WGS and found that all four methods were suitable to varying degrees for determining gene copy numbers. The strengths and limitations of each technique are discussed, and the authors suggest prioritizing dPCR and PE-WGS for precise analysis. The document also provides references and supporting information for three related articles, which can be helpful for library patrons researching agricultural biotechnology, PCR techniques, and structural variation studies in plants. [Extracted from the article]

Turmeric (Curcuma longa L.), a well-documented medicative plant, is used as a foodstuff, cosmetic, and medicine. The objective of this study was to assess the influence of mineral fertilizers on the phytochemical evaluation, curcumin, flavonoids, and total protein contents of turmeric (Curcuma longa L.) rhizomes grown in different regions of Uzbekistan. The experiments were carried out in a randomized block design with three replications: a mini plot experiment at the Institute of Genetics and Plant Experimental Biology in the Kibray district, Tashkent region, and a field experiment at the Surkhandarya Scientific Experimental Station of the Vegetable, Melon Crops, and Potato Research Institute, Uzbekistan. The experimental treatments included: T1 - control (without fertilizer), T2 - NPK treatment (application rate 75:50:50 kg/ha), T3 - NPK treatment (application rate 125:100:100 kg/ha), and T4 - NPK + BZnFe treatment (application rate 100:75:75:3:6:6 kg/ha). At harvest, after eight months, the phytochemical properties, curcumin, flavonoids, and total protein content of the turmeric rhizomes were determined. The results revealed the presence of alkaloids, terpenoids, tannins, flavonoids, steroids, carbohydrates, and saponins in the methanolic extract of turmeric rhizomes grown in different regions (Tashkent and Surkhandarya). The chloroform extract showed the presence of six phytochemicals, including alkaloids, terpenoids, flavonoids, steroids, carbohydrates, and saponins in the rhizomes of turmeric collected from both regions, Tashkent and Surkhandarya. However, the NPK + BZnFe treatment (application rate 100:75:75:3:6:6 kg/ha) significantly increased the curcumin, rutin, and quercetin contents of turmeric rhizomes grown in the Tashkent and Surkhandarya regions. The highest total protein content was recorded in the NPK kg/ha treatment (application rate 125:100:100 kg/ha), showing a significant increase compared to the control. It was concluded that the NPK + BZnFe treatment (application rate 100:75:75:3:6:6 kg/ha) significantly increased the curcumin and flavonoid contents of turmeric rhizomes grown in the Tashkent and Surkhandarya regions compared to the control. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Studies that show how empire influenced the development of plant genetics add to the established history of genetics and 20th‐century agricultural science. One approach to broadening this history is to consider the contributions of students studying abroad and their greater careers back home. Research agendas differed between and within institutions, much as they do today. This article explores the postgraduate education of an Indian groundnut breeder. It highlights the structural challenges faced by researchers at agricultural departments who sought promotion through education and examines the consequences for plant breeding and for farmers. Summary: Through the biography of V.K. Badami, this article contributes to debates about genetics and plant breeding in the history of science. Badami, an accomplished breeder in the Mysore Department of Agriculture, took a leave to study genetics at the University of Cambridge. His professors nearly failed him, yet Badami's groundnut breeding experiments proved influential for Indian farmers as well as advances in crop science. This history adds to the thesis that academic genetics varied in support of professional plant breeding by comparing institutional expections between Mysore and Cambridge.The argument is developed by reading Badami's student records along with his groundnut breeding experiments in South India.The study connects the disciplinary history of genetics to plant breeding for the British empire.Badami's experience at Cambridge is indicative of the power relationship between academic genetics and imperial plant breeding in the early 20th century. In this case, his commitments as an Indian agricultural officer conflicted with the discipline's devotion to quantitative analysis. [ABSTRACT FROM AUTHOR]

The commercial cultivation of genetically modified (GM) crops has eased the global food crisis and brought considerable economic and social benefits to countries. Because of the potential safety problems, it is necessary to make clear the molecular genetic characteristics, edible safety, planting, processing, and other aspects of the safety evaluation of GM crops. The safety problems existing in the cultivation of GM crops, safety evaluation and detection of GM crops were introduced in this paper, which provided the basis for safety evaluation and effective supervision of GM crops and their products. Commercial cultivation and reasonable supervision based on safety evaluation have far-reaching significance for ensuring consumer safety, enhancing the credibility of the national political system and enhancing citizens' confidence in the safety of GM crop products for consumption. [ABSTRACT FROM AUTHOR]

The yield and concentration of secondary metabolites (SMs) in plants can vary due to numerous challenges such as dynamic environmental conditions, moisture, soil quality, soil organic matter and plant genetics. To obtain a good yield of SMs novel elicitation approaches, such as the use of biotic and abiotic stressors, genetic modifications, and optimized growth conditions, have been practiced, particularly the use of selenium nanoparticles (SeNPs) and light emitting diode (LED) interaction through employing tissue culture technique. In the present study, in vitro callus cultures of sandalwood (Santalum album L.) were subjected to elicitation with different concentrations of SeNPs with doses of 30 µg/L, 60 µg/L, and 90 µg/L in combination with green (∼550 nm), red (∼660 nm) and blue (∼460 nm) LED lights. Interaction of these treatments produced 16 treatments replicated three times in 48 test tubes. The results were analysed using two-way ANOVA and Tukey's HSD test. The study revealed that synergistic interaction between SeNPs and LED light wavelengths significantly enhanced callus growth and secondary metabolite (SM) production eliciting callus cultures with blue LED light and a dose of 90 µg/L SeNPs resulted in an increase in callus growth including fresh weight, dry weight, and the number of shoot branches per callus. This combined treatment positively influenced the functions of major bioactive antioxidants such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and phenylalanine ammonia-lyase (PAL). Furthermore, the concentrations of essential secondary metabolites, including total phenolic, total saponins, casein/BSA/PVPP-bound tannins, flavan-3-ols, and tocopherols experienced substantial elevation under the synergistic influence of SeNPs and LED light conditions. The sandalwood plants produced through the callus culturing technique using optimized SeNPs and LED lights show an enhanced yield of secondary metabolites, which will be very useful and potential for pharmaceutical, cosmetic and various other industries to discover and develop novel products. [ABSTRACT FROM AUTHOR]

Simple Summary: Four Vietnamese breeding lines (2 Japonica and 2 Indica) were directly compared in field settings for phenotypic traits associated with yield. These Vietnamese rice genomes were newly de novo assembled and annotated, and a phylogenetic analysis of the phytochrome C (phyC) confirmed the positioning and diversity between the four varieties. The four lines showed enough phenotypic and genetic differences to be used as parental lines for climate-adaptation breeding programs. This study begins by examining phenotypic variations in field growth among four parental Vietnamese rice lines, consisting of two Indica (PD211/GL37) and two Japonica (J23/SRA2-1) cultivars, which differ in life-cycle durations. Their phenotypic observations revealed both similarities and differences in growth patterns and field responses, setting the stage for further genomic investigation. We then focused on the sequencing and de novo genome assembly of these lines using high-coverage Illumina sequencing and achieving pseudochromosome assemblies ranging between 379 Mbp and 384 Mbp. The assemblies were further enhanced by annotation processes, designating between 44,427 and 48,704 gene models/genome. A comparative genomic analysis revealed that the Japonica varieties (J23/SRA2-1) exhibited more genetic similarity than the Indica varieties (PD211/GL37). From this, a phylogenetic analysis on the phytochrome C (phyC) gene distinctly positions the Indica and Japonica lines within their respective clades, affirming their genetic diversity and lineage accuracy. These genomic resources will pave the way for identifying quantitative trait loci (QTLs) critical for developing rice cultivars with shorter life cycles, thus enhancing resilience to adverse climatic impacts in Vietnam. This study provides a foundational step towards leveraging genomic data for rice breeding programs aimed at ensuring food security in the face of climate change. [ABSTRACT FROM AUTHOR]

The three 31 nucleotide minihelix tRNA evolution theorem describes the evolution of type I and type II tRNAs to the last nucleotide. In databases, type I and type II tRNA V loops (V for variable) were improperly aligned, but alignment based on the theorem is accurate. Type II tRNA V arms were a 3′-acceptor stem (initially CCGCCGC) ligated to a 5′-acceptor stem (initially GCGGCGG). The type II V arm evolved to form a stem–loop–stem. In Archaea, tRNALeu and tRNASer are type II. In Bacteria, tRNALeu, tRNASer, and tRNATyr are type II. The trajectory of the type II V arm is determined by the number of unpaired bases just 5′ of the Levitt base (Vmax). For Archaea, tRNALeu has two unpaired bases, and tRNASer has one unpaired base. For Bacteria, tRNATyr has two unpaired bases, tRNALeu has one unpaired base, and tRNASer has zero unpaired bases. Thus, the number of synonymous type II tRNA sets is limited by the possible trajectory set points of the arm. From the analysis of aminoacyl-tRNA synthetase structures, contacts to type II V arms appear to adjust allosteric tension communicated primarily via tRNA to aminoacylating and editing active sites. To enhance allostery, it appears that type II V arm end loop contacts may tend to evolve to V arm stem contacts. [ABSTRACT FROM AUTHOR]

Diospyros mun A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of D. mun's genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of D. mun. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within D. mun germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of D. mun in Vietnam. In this study, the transcriptomes of D. mun were analysed using the Illumina HiSeqTM 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. De novo assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult D. mun trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with PIC = 0.77, NA = 3.9, NE = 2.8, Ho = 0.56 and HE = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (FST = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient D. mun from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of D. mun. [ABSTRACT FROM AUTHOR]

On February 12, 2024, Academician of the Russian Academy of Sciences Vladimir Konstantinovich Shumny turned 90 years old. V.K. Shumny from 1985 to 2007 headed the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (ICG SB RAS). For more than 30 years he was the head of the Department of Cytology and Genetics of the Faculty of Natural Sciences of Novosibirsk State University and the chairman of the dissertation council of the Institute of Cytology and Genetics SB RAS. Since 1980, he was a member of the Presidium of the Siberian Branch of the USSR Academy of Sciences / RAS, since 1986 he became deputy chairman, and since 1992 - chairman of the Joint Scientific Council of the SB RAS for biological sciences. Since 2004 V.K. Shumny headed the Vavilov Society of Genetics and Breeders (VOGiS) for 10 years, and since 2014 he has been the honorary president of this society. For more than 20 years V.K. Shumny was the editor-in-chief of the periodical scientific publication “VOGiS Herald” (now the Vavilov Journal of Genetics and Selection). The scientific activity of V.K. Shumny is related to plant genetics. He is the head of one of the largest scientific schools in this field. Under his leadership, 6 doctors and 24 candidates of science defended their dissertations. He has published more than 500 scientific papers and received 12 copyright certificates for plant varieties. V.K. Shumny is co-author and editor of several school textbooks on biology.

This document is an editorial from the journal Frontiers in Plant Science that emphasizes the importance of conserving genetic resources for crop improvement and biodiversity. It discusses the availability of genomic tools and technologies for studying diversity and supporting conservation efforts. The document includes summaries of various research articles on topics such as genetic diversity in olive germplasm, genomic characterization of wheat crop wild relatives, and genetic diversity of Albizia odoratissima. It also acknowledges the lack of reports from Africa but highlights the active work being done in China. The document concludes by stating that while there is a strong molecular emphasis in the research, the challenges of managing genetic resources remain the same. [Extracted from the article]

The article assesses the genetic diversity of wild edible mushrooms (WEM) in the East Siang district of Arunachal Pradesh using simple sequence repeat markers. The study analyzes the polymorphism among the strains of WEM, including polymorphic alleles and polymorphic information content, as well as the genetic variation and similarity among WEN varieties.

This article explores the role of LysM receptors, specifically LYS6 and LYS7, in regulating arbuscular mycorrhiza (AM) in Lotus japonicus. AM is a beneficial interaction between plants and fungi that aids in nutrient exchange. The study found that LYS7 is upregulated in roots infected with AM fungi, suggesting its involvement in AM. Mutants lacking LYS6 and LYS7 showed reduced colonization and arbuscule formation by AM fungi, highlighting the importance of these receptors in AM regulation. The study also revealed that LYS6 is involved in the expression of AM-induced genes and the induction of calcium spiking. Overall, LYS6 and LYS7, along with their downstream signaling pathways, are crucial for the initial response to AM in Lotus japonicus. [Extracted from the article]

Improved understanding of the complex interaction between plant metabolism, environmental conditions and the plant-associated microbiome requires an interdisciplinary approach: Our hypothesis in our multiomics study posited that several environmental and biotic factors have modulating effects on the microbiome and metabolome of the roots of wild Echium vulgare plants. Furthermore, we postulated reciprocal interactions between the root metabolome and microbiome. We investigated the metabolic content, the genetic variability, and the prokaryotic microbiome in the root systems of wild E. vulgare plants at rosette and flowering stages across six distinct locations. We incorporated the assessment of soil microbiomes and the measurement of selected soil chemical composition factors. Two distinct genetic clusters were determined based on microsatellite analysis without a consistent alignment with the geographical proximity between the locations. The microbial diversity of both the roots of E. vulgare and the surrounding bulk soil exhibited significant divergence across locations, varying soil pH characteristics, and within the identified plant genetic clusters. Notably, acidophilic bacteria were characteristic inhabitants of both soil and roots under acidic soil conditions, emphasizing the close interconnectedness between these compartments. The metabolome of E. vulgare significantly differed between root samples from different developmental stages, geographical locations, and soil pH levels. The developmental stage was the dominant driver of metabolome changes, with significantly higher concentrations of sugars, pyrrolizidine alkaloids, and some of their precursors in rosette stage plant roots. Our study featured the complex dynamics between soil pH, plant development, geographical locations, plant genetics, plant metabolome and microbiome, shedding light on existing knowledge gaps. [ABSTRACT FROM AUTHOR]

The article presents a study which identified the role that environmental factors play in explaining the heritability of important economic traits across a range of rice bean genotypes cultivated under different settings. Topics include genotypic and phenotypic coefficient of correlation, genotypic character association among yield and yield contributing traits in rice bean, and phenotypic path coefficient analysis among yield and yield contributing traits in rice bean.

The article presents a study which evaluated 30 Niger (Guizotia abyssinica) genotypes for ten quantitative traits using germplasm obtained from ZARS, Igatpuri, during the Kharif season of 202 at the College of Agriculture, Pune, Maharashtra in India. Topics discussed include classifications of the genotypes based on their genetic characteristics, distribution of Niger genotypes into different clusters, and percent contribution of ten characters for divergence in Niger.

The article presents a study which assessed the genetic variability of cotton germplasm and land races using temperature induction response (TIR) to identify more sources for intrinsic tolerance and to identify the genotypes that combine temperature tolerance with tolerance of drought stresses. Topics include standardization of optimum induction temperature and challenging high temperature for cotton seedlings and percent mortality of cotton seedlings at different lethal temperatures.

The article presents a study which investigated the genetic factors influencing yield in eggplant (Solanum melongena L) hybrids under organic cultivation conditions in India. Topics include genetic and phenotypic variations of India's primary origin for eggplant, effects of genotypes on yield and other characters in eggplant, and estimation of heterosis over the better parent and heck variety (PPL) for yield and other different characters in eggplant.

The article presents a study on the genetic parameters for yield and its component traits in urd bean of Vigna mungo L. Hepper, one of the important pulse crops in India. Topics include genetic variability for all characters, estimates of heritability for all the traits, and path coefficient analysis at phenotypic level.

The article presents a study which aimed at revealing the reproductive characters and establishing a set of breeding parameters for genetic improvement using morphological markers of annatto (Bixa orellana L). Topics discussed include quantification of total phenolic content and of total flavonoids, culture preparation and determination of minimal inhibitory concentration (MIC), and characterization of annatto using morphological markers.

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Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is a precious and scarce tree species resource in the East China region. To comprehend the origin, evolutionary history, geographical, and historical factors that has contributed to the current distribution pattern of Phoebe chekiangensis in the East China region, we conducted a phylogeographic analysis that utilized intergenic spacers of chloroplast DNA (cpDNA). We amplified and sequenced three spacer regions of cpDNA (psbC-trnS, trnL-Intro, and Ycf3) intergenic spacer regions of 306 individuals from 11 populations, encompassing the majority of its geographical range in China. Our analysis revealed a total of 11 haplotypes. The research findings show that the spacer regions of the cpDNA genetic diversity of Phoebe chekiangensis was Hd = 0.423, and the nucleotide diversity was Pi × 10−3 = 0.400. At the species level, the population differentiation index Fst = 0.25610 (p < 0.05), and the gene flow Nm = 0.73. The genetic variation between populations was 29.14%, while within populations, it was 70.86%, with the inter-population genetic variation much lower than the within-population variation. The divergence time between the genera Phoebe and Machilus was estimated to be approximately 37.87 mya (PP = 1; 95%HPD: 25.63–44.54 mya), and the crown group time of the genus Phoebe was estimated to be 21.30 mya (PP = 1; 95%HPD: 9.76–34.94 mya). The common ancestor of the 11 Phoebe chekiangensis haplotypes was 7.85 mya, while the H7, H8, and H10 haplotypes of Phoebe chekiangensis (northern region) differentiated relatively late, with a divergence time of 1.90 mya. Neutrality tests (NTs) and mismatch distribution analysis (MDA) suggest that the time frame for Phoebe chekiangensis to expand southwestward along Wuyishan was relatively short and its adaptability to the environment was low, thereby limiting the formation of new haplotypes. These results suggest that Phoebe chekiangensis exhibited greater adaptation to the northern subtropics than to the central subtropics, offering valuable insights for the conservation and utilization of germplasm resources. [ABSTRACT FROM AUTHOR]

To estimate the extent of genetic diversity of 56 Pearl millet genotypes for eight morphological characters, an experiment was carried out at the research farm of Forage Section, Department of Genetics & Plant Breeding, CCS HAU, Hisar in kharif 2020-21. In Principal component analysis (PCA) the eigenvalues were used to determine how many factors to retain. In the present study, the first four principal components (PCs) had eigen values greater than one, and they cumulatively explained 71.3% of the total variation present in the original dataset. The first principal component (PC 1) explained 20.30% of the total variability, while the PC 2, PC 3, and PC 4 explained 19.2%, 17.3%, and 14.5% of the total variability, respectively. O 54, O 34, O 25, O 15, and O 40 were found as the topranking genotypes upon PCA analysis with high positive PC1 scores. These genotypes, showed highest overall mean values for the traits positively related to grain yield and its attributing traits. These findings can be useful in formulating breeding strategies for future hybridization programs for yield improvement and are appropriate for classification of diversity among pearl millet germplasm. [ABSTRACT FROM AUTHOR]

Simple Summary: In Kazakhstan, tulips are not just beautiful flowers but also vital to the environment, with 35 species, 18 of which are protected. Recent research near Kazakhstan's borders uncovered new tulip varieties, highlighting the need for a species inventory. In this study, we identified eight tulip species using both physical traits and advanced DNA testing. By analyzing genetic markers, we discovered that certain DNA regions are particularly useful for identifying tulip species. However, when it comes to closely related tulips, combining data from multiple DNA markers is crucial for accurate classification. This study also unveiled possible natural hybrids, indicating complex interactions between different tulip species. This research sheds light on the diversity and evolutionary relationships among tulips, providing valuable insights for conservation efforts and understanding plant genetics. Further investigations into tulip populations are necessary to confirm these findings and better protect these precious flowers. In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis. [ABSTRACT FROM AUTHOR]

Summary: Floral nectar composition beyond common sugars shows great diversity but contributing genetic factors are generally unknown. Mānuka (Leptospermum scoparium) is renowned for the antimicrobial compound methylglyoxal in its derived honey, which originates from the precursor, dihydroxyacetone (DHA), accumulating in the nectar. Although this nectar trait is highly variable, genetic contribution to the trait is unclear. Therefore, we investigated key gene(s) and genomic regions underpinning this trait.We used RNAseq analysis to identify nectary‐associated genes differentially expressed between high and low nectar DHA genotypes. We also used a mānuka high‐density linkage map and quantitative trait loci (QTL) mapping population, supported by an improved genome assembly, to reveal genetic regions associated with nectar DHA content.Expression and QTL analyses both pointed to the involvement of a phosphatase gene, LsSgpp2. The expression pattern of LsSgpp2 correlated with nectar DHA accumulation, and it co‐located with a QTL on chromosome 4. The identification of three QTLs, some of the first reported for a plant nectar trait, indicates polygenic control of DHA content.We have established plant genetics as a key influence on DHA accumulation. The data suggest the hypothesis of LsSGPP2 releasing DHA from DHA‐phosphate and variability in LsSgpp2 gene expression contributing to the trait variability. [ABSTRACT FROM AUTHOR]

Soybean is an important legume crop and a major source of nutrients in Nigeria. However, there is a need to compare some breeding lines for their nutritional qualities. This study evaluated the nutritional qualities of three soybean varieties (TGX1987-10F, TGX2018-1E, TGX2024-3E) as part of breeding lines undergoing genetic improvement at the Joseph Sarwuan Tarka University, Makurdi, Nigeria. The composition of soybeans was found to be dominated by carbohydrates (34.4%), followed by protein (24.44%), lipid (27.5%), moisture (6.2%), ash (4.5%), and fiber (3.3%). Among the varieties, TGX1987-10F exhibited the highest levels of carbohydrate, protein, and fiber. Conversely, TGX2024-3E displayed the highest moisture, ash, and lipid contents. TGX2018-1E occupied an intermediate position between the two varieties in terms of proximate values. There were no significant differences in the levels of anti-nutrients (cyanide and oxalate) among the varieties. However, phytic acid content varied significantly, with TGX2024-3E having the lowest amount and TGX1987-10F having the highest. Phytic acid showed a negative correlation with all nutrients except carbohydrate. These findings suggest that TGX1987-10F is the variety with the highest overall nutritional value, but it also has the highest level of phytic acid. Breeders should aim to improve the nutritional quality of soybean while also reducing anti-nutrients. This information is important for breeders and farmers who are working to ensure food abundance and quality. [ABSTRACT FROM AUTHOR]

Diospyros spp. is a tree or shrub species belonging to the family Ebenaceae. Researchers have not extensively conducted studies on the morphological characteristics of Diospyros spp. to examine their diversity or enhance information for taxonomic hierarchy purposes. Diospyros spp. in Indonesia has great potential for in-depth research due to its unique characteristics, particularly in Sulawesi. This research aims to fill the knowledge gap regarding investigating phenotypic variations in Diospyros spp., specifically in the Sulawesi region. Nine species of Diospyros spp. from the Bogor Botanical Gardens collection were observed for their morphological characteristics and described according to their character traits. The results indicate 25 variations in morphological characteristics out of the 50 characters used. These 14 characteristics are key characteristics that influence the grouping of Diospyros spp. from Sulawesi. Phenetic analysis generates three clades of 9 accessions Diospyros spp. analyzed. [ABSTRACT FROM AUTHOR]

In this study, we examined over 200-year-old Ginkgo biloba L. specimens under different environmental conditions. The overall aim was to explore which factors influence their vitality and general fitness in urban environments and thus their ability to tolerate stressful habitats. In order to determine this, we used a number of different methods, including histological examinations (stomatal density and size) and physiological measurements (peroxidase enzyme activity), as well as assessing the air pollution tolerance index (APTI). The investigation of the genetic relationships between individuals was performed using flow cytometry and miRNA marker methods. The genetic tests revealed that all individuals are diploid, whereas the lus-miR168 and lus-miR408 markers indicated a kinship relation between them. These results show that the effect of different habitat characteristics can be detected through morphological and physiological responses, thus indicating relatively higher stress values for all studied individuals. A significant correlation can be found between the level of adaptability and the relatedness of the examined individuals. These results suggest that Ginkgo biloba L. is well adapted to an environment with increased stress factors and therefore suitable for use in urban areas. [ABSTRACT FROM AUTHOR]

Phalaenopsis is one of the most well-known genera of the orchid family and has relatively good growth due to its high adaptability. The Phalaenopsis breeding program and full investigation of progenies takes three to five years, which can be reduced by using molecular markers. In this research, in order to decrease the process of selecting superior genotypes, progenies obtained from crosses between 5 different cultivars were examined using IRAP and RAPD markers. Among 299 bands produced in RAPD, 86% of the bands were polymorphic. The average number of polymorphic bands was 13.5 bands per primer and the minimum genetic similarity (43%) was obtained between 'Sevilla'x'Sevilla' and 'Manila'x'Bombay' hybrids, while the maximum similarity (72%) was found between 'Sevilla'x 'Okayama' and 'Okayama'x'Sevilla' hybrids based on Nei similarity coefficient. From 6 selected IRAP primer combinations, 83 bands were produced, among them 72 bands were considered polymorphic bands. The highest ratio of polymorphism was obtained by 3'LTRLTR6150, 3'LTR-3'LTR primers combination and the lowest by Sukkula -3'LTR. The maximum genetic similarity, 82%, using IRAP marker was observed between 'Sevilla'x'Okayama' and 'Sevilla'x'Manila' hybrids and the lowest amount, 32%, was obtained between 'Sevilla'x'Sevilla' and 'Manila'x'Bombay' hybrids, indicating the genetic proximity and distance, respectively, of the studied genotypes. Recombined genotypes obtained in this research, which had different band patterns with their parents, can be used for breeding programs and introducing new cultivars. [ABSTRACT FROM AUTHOR]

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The present investigation was undertaken at the Hybrid Rice plot of TCA, Dholi, and Muzaffarpur, and molecular analysis was conducted in the Molecular Laboratory of Postgraduate Dept. of Genetics & Plant Breeding, RPCAU, and Bihar to generate heterosis studies for 18 traits and molecular characterization using SSR markers. The experimental material comprised 31 three-line rice hybrids and 3 commercial checks evaluated in the RBD design. Among the tested varieties, Rajendra Sweta performed best in terms of grain yield per plant. Two rice hybrid genotypes, namely, IR68897A × KMR-3R and Rajendra-3A × RRR–4, exhibited superior standard heterosis over all three tests for trait grain yield per plant. By utilizing 12 primer pairs, a total of 33 shared alleles and 13 unique alleles were produced as amplified products. Among the 12 primers, seven primers were found to be comparatively informative for all nineteen hybrids and eleven parents. Only five primers, namely, MRG2894, RM515, RM520, RM538, and RM555, were able to confirm the hybridity (F1) with the respective parental lines. [ABSTRACT FROM AUTHOR]

Summary: The invasive character of Eichhornia crassipes (water hyacinth) is a major threat to global biodiversity and ecosystems. To investigate the genomic basis of invasiveness, we performed the genome and transcriptome sequencing of E. crassipes and reported the genome of 1.11 Gbp size with 63,299 coding genes and N50 of 1.98 Mb. We confirmed a recent whole genome duplication event in E. crassipes that resulted in high intraspecific collinearity and significant expansion in gene families. Further, the orthologs gene clustering analysis and comparative evolutionary analysis with 14 other aquatic invasive and non-invasive angiosperm species revealed adaptive evolution in genes associated with plant-pathogen interaction, hormone signaling, abiotic stress tolerance, heavy metals sequestration, photosynthesis, and cell wall biosynthesis with highly expanded gene families, which contributes toward invasive characteristics of the water hyacinth. However, these characteristics also make water hyacinth an excellent candidate for biofuel production, phytoremediation, and other translational applications.

The article discusses advancements in the design and application of hydrogels, particularly in biomedical fields, focusing on the integration of semiconducting functionalities through solvent exchange methods. Topics discussed include the impact of agrochemicals on insect populations, the rapid spread of wildfires in the U.S., and innovative approaches to protein design using machine learning techniques.

The article "QUIC-seq: Quick ultra-affordable high-throughput convenient RNA sequencing" introduces a new method for gene expression analysis called QUIC-seq, which is quick, cost-effective, and suitable for high-throughput applications. The method involves extracting RNA, reverse transcription, Tn5 transposase fragmentation, and direct PCR amplification. QUIC-seq simplifies library construction, reduces costs, and offers high reproducibility. The method was used to identify differentially expressed genes in response to nitrogen and phosphorus stress, as well as in exploring gene regulatory networks. QUIC-seq is compared to other RNA-seq methods, showing advantages in cost, throughput, and efficiency. [Extracted from the article]

Warburgia ugandensis and Saururus chinensis are two of the most important medicinal plants in magnoliids and are widely utilized in traditional Kenya and Chinese medicine, respectively. The absence of higher-quality reference genomes has hindered research on the medicinal compound biosynthesis mechanisms of these plants. We report the chromosome-level genome assemblies of W. ugandensis and S. chinensis, and generated 1.13 Gb and 0.53 Gb genomes from 74 and 27 scaffolds, respectively, using BGI-DIPSEQ, Nanopore, and Hi-C sequencing. The scaffold N50 lengths were 82.97 Mb and 48.53 Mb, and the assemblies were anchored to 14 and 11 chromosomes of W. ugandensis and S. chinensis, respectively. In total, 24,739 and 20,561 genes were annotated, and 98.5% and 98% of the BUSCO genes were fully represented, respectively. The chromosome-level genomes of W. ugandensis and S. chinensis will be valuable resources for understanding the genetics of these medicinal plants, studying the evolution of magnoliids and angiosperms and conserving plant genetic resources. [ABSTRACT FROM AUTHOR]

Plants of the Caprifoliaceae family are widely cultivated worldwide as ornamental plants owing to their numerous, sweet-smelling, beautiful flowers and fruits. Heptacodium miconioides Rehd., a member of the family, is endemic to eastern China and is cultivated as a popular ornamental plant in North America and European countries. It has a rather novel and beautiful trait of high horticultural value, that is, its sepals persist and enlarge, turning purplish red. Here, we report the chromosome-level genome assembly of H. miconioides to understand its evolution and floral characteristics. The 622.28 Mb assembled genome harbored a shared whole-genome duplication with a related species, Lonicera japonica. Comparative genomic analysis suggested that chromosome fission events following genome duplication underlie the unusual chromosome number of these two species, as well as chromosome fission of another five chromosomes in H. miconioides, giving rise to a haploid chromosome number of 14 (versus 9 in L. japonica). In addition, based on transcriptome and chloroplast genome analysis of 17 representative species in the Caprifoliaceae, we assumed that large structural variations in the chromosomes of H. miconioides were not caused by hybridization. Changes in the candidate genes of the MADS-box family were detected in the H. miconioides genome, including AP1-, AP3-, and SEPexpanded, which might underlie the sepal elongation and development in this species. The current findings provided a critical resource for genome evolution studies in Caprifoliaceae and it was an example of how multi-omics data can elucidate the regulation of important ornamental traits. [ABSTRACT FROM AUTHOR]

Host–plant resistance (HPR) is a subdiscipline in entomology that aims to understand, develop, and deploy crop varieties resistant to arthropod herbivores. The seminal figure in HPR was Reginald Painter, whose 1951 monograph Insect Resistance in Crop Plants established a conceptual framework and methodological approach for applied research on plant resistance. In the 75 years since the publication of this book, the empirical and multidisciplinary approach established by Painter has led to the development and use of hundreds of arthropod-resistant crop varieties. Much of the success of HPR research has been, and will continue to be, tied to advances in scientific disciplines related to HPR, such as plant breeding and genetics, analytical chemistry, and plant–insect interactions. However, given the challenges facing agriculture and pest management over the coming decades, increased attention will need to be given to the deployment of resistant varieties and the integration of resistant varieties into integrated pest management (IPM) programs. Recent advances in our understanding of fundamental aspects of the interactions between plants and herbivores provide insights that can facilitate the increased use of plant resistance in IPM programs, and the diverse membership of the Entomological Society of America can play a critical role by increasing communication between scientists interested in applied and fundamental aspects of plant resistance to insects. [ABSTRACT FROM AUTHOR]

In the post-genomic era, virus-induced gene silencing (VIGS) has played an important role in research on reverse genetics in plants. Commonly used Agrobacterium-mediated VIGS inoculation methods include stem scratching, leaf infiltration, use of agrodrench, and air-brush spraying. In this study, we developed a root wounding-immersion method in which 1/3 of the plant root (length) was cut and immersed in a tobacco rattle virus (TRV)1:TRV2 mixed solution for 30 min. We optimized the procedure in Nicotiana benthamiana and successfully silenced N. benthamiana, tomato (Solanum lycopersicum), pepper (Capsicum annuum L.), eggplant (Solanum melongena), and Arabidopsis thaliana phytoene desaturase (PDS), and we observed the movement of green fluorescent protein (GFP) from the roots to the stem and leaves. The silencing rate of PDS in N. benthamiana and tomato was 95-100%. In addition, we successfully silenced two disease-resistance genes, SITL5 and SITL6, to decrease disease resistance in tomatoes (CLN2037E). The root wounding-immersion method can be used to inoculate large batches of plants in a short time and with high efficiency, and fresh bacterial infusions can be reused several times. The most important aspect of the root wounding-immersion method is its application to plant species susceptible to root inoculation, as well as its ability to inoculate seedlings from early growth stages. This method offers a means to conduct large-scale functional genome screening in plants. [ABSTRACT FROM AUTHOR]

Plant diseases cause famines, drive human migration, and present challenges to agricultural sustainability as pathogen ranges shift under climate change. Plant breeders discovered Mendelian genetic loci conferring disease resistance to specific pathogen isolates over 100 years ago. Subsequent breeding for disease resistance underpins modern agriculture and, along with the emergence and focus on model plants for genetics and genomics research, has provided rich resources for molecular biological exploration over the last 50 years. These studies led to the identification of extracellular and intracellular receptors that convert recognition of extracellular microbe-encoded molecular patterns or intracellular pathogen-delivered virulence effectors into defense activation. These receptor systems, and downstream responses, define plant immune systems that have evolved since the migration of plants to land ∼500 million years ago. Our current understanding of plant immune systems provides the platform for development of rational resistance enhancement to control the many diseases that continue to plague crop production. Plant diseases significantly impact human and environmental health. This review encompasses the last 50 years of research in the plant immune system, an overview of the pathogen virulence proteins, and strategies for durable resistance. [ABSTRACT FROM AUTHOR]

Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework. [ABSTRACT FROM AUTHOR]

As robotic systems become increasingly integrated into plant phenotyping processes, the quality of images captured plays an increasingly crucial role in accurate data collection and analysis. Here we address the challenge of assessing and enhancing image quality in the context of plant phenotyping robot using a pan-tilt-zoom camera. We present a data-driven approach using machine learning, specifically the Random Forest classifier, to classify both blurred and sharp images. Our method involves feature extraction, data preprocessing, hyperparameter tuning, and cross-validation. The resulting model demonstrates promising performance as indicated by its accuracy, precision, recall, area under the curve (AUC), and feature importance analysis. Notably, our results support a highly accurate classifier, achieving a correct classification rate of 95% for sharp images and 92% for blurred ones, a receiver operating characteristic curve with an AUC of 0.93, and a precision-recall curve with an average precision of 0.91. Shapley Additive Explanations analysis identifies "edge density" and "mean gradient magnitude" as influential to the classifier, offering valuable insights for future feature engineering and model refinement. The classifier has a short inference time (2.8 s) on a Raspberry Pi 4B computer, both improving the quality of captured images and automatically eliminating blurred images. By enhancing image quality assessment, this research improves data reliability and the overall effectiveness of plant phenotyping robots. We discuss the implications of these findings and their practical relevance and suggest directions for future research. [ABSTRACT FROM AUTHOR]